From owner-structural-nmr@net.bio.net Tue Oct 01 23:00:00 1996 Path: biosci!chem.umu.se!ingmar.sethson From: ingmar.sethson@chem.umu.se (Ingmar Sethson) Newsgroups: bionet.structural-nmr Subject: position available Date: 2 Oct 1996 06:00:51 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 52 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters, The following position (as described in the accompanying ad) is available at Ume=E5 University in Sweden: RESEARCH POSITION AVAILABLE A permanent position is available at the Department of Medical Biophysics, Ume=E5 University. This position will be shared equally between the Departments of Medical Biophysics and Organic Chemistry. The successful candidate, a graduated NMR scientist (Ph.D.), preferably with post-doctoral experience, will be responsible for the management of high resolution NMR equipment, consisting initially of a Bruker DRX600 to be installed in December of this year (1996), an AMX2 500 and an ACP250 NMR spectrometer. The successful candidate should have excellent experience and an interest in NMR methodology and equipment. The successful candidate will have the opportunity to perform own research in the field of biological NMR and/or participate in ongoing biological NMR projects focusing on the structure determination of biological molecules, such as peptides, proteins and nucleic acids, and on the study of their interactions, by using NMR techniques. Ume=E5 University applies individual salary-setting. Applications, quoting the appropriate reference number (3135-1647-96) together with a Curriculum Vitae and the names and addresses of two professional referees, should reach the Registrar, Ume=E5 University, S-901 87 Ume=E5, Sweden, not later than 1 December, 1996. =46urther information can be obtained from Professor Sybren Wijmenga, Department of Medical Biophysics, Ume=E5 University, S-901 87 Ume=E5, Sweden= , tel.: +46-90-167403/165234, e-mail: sybren@indigo.chem.umu.se and/or Professor Ulf Edlund, Department of Organic Chemistry, Ume=E5 University, tel.; +46-90-166933, e-mail: ulf.edlund@chem.umu.se. ingmar sethson =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Ingmar Sethson Dep. Organic Chemistry Ume=E5 University S-901 87 Ume=E5, Sweden E-mail: ingmar.sethson@chem.umu.se Ph. nr.: +46-90-16 62 86 =46ax. nr.: +46-90-13 88 85 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D From owner-structural-nmr@net.bio.net Tue Oct 01 23:00:00 1996 Path: biosci!charnwood.gb.astra.com!Mark.J.M.Dixon From: Mark.J.M.Dixon@charnwood.gb.astra.com (Mark Dixon, Tel +44 1509 644 062) Newsgroups: bionet.structural-nmr Subject: Solubilizing proteins Date: 2 Oct 1996 16:53:00 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 30 Sender: daemon@net.bio.net Distribution: world Message-ID: <"13435120016991.149557.MRX*"@MHS> NNTP-Posting-Host: net.bio.net We have a 12kDa cytoplasmic protein which is insoluble in aqueous media at NMR concentrations, we would prefer a MINIMUM of 1 mmol in 0.5 ml. We thought about using a percentage of trifluoroethanol ( TFE ), but this appears to have a "side-effect" of instilling alpha-helical structure in unstructured loops and bends. Our protein is about 90% alpha-helical already in four bundles connected by loops. Any more helicity and we will lose tertiary structure and end up with a helical rod !! Not good. SDS micelles and/or high temperature are not an option. Can anyone suggest a method of solubilizing proteins up to NMR concentrations without modifications to the tertiary structure. We are amenable to additives, but obviously the fewer the better. If a large number of responses are posted to me, I will create a summary for the list. Thank you, Mark Dixon Astra Charnwood mark.j.m.dixon@charnwood.gb.astra.com From owner-structural-nmr@net.bio.net Tue Oct 01 23:00:00 1996 Path: biosci!chem.umu.se!ingmar.sethson From: ingmar.sethson@chem.umu.se (Ingmar Sethson) Newsgroups: bionet.structural-nmr Subject: Position available, again Date: 2 Oct 1996 14:44:21 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 301 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net --============_-1367822507==_============ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable I'm sorry for the way the one of the Swedish vowels appeared in the previos mail about the NMR postion available in Umea (located in the north of Sweden). The a in Umea should look like an 'a' with a small circle on top of it. For those of you who are interested in getting a proper view of the ad, I've attached the ad as an attached Word document (done with Eudora). ingmar sethson --============_-1367822507==_============ Content-Type: application/mac-binhex40; name="RESENG.DOC" Content-Disposition: attachment; filename="RESENG.DOC" (This file must be converted with BinHex 4.0) :#P*&8d914bj%6d-!9d4#6Ne69d3!!!!!-!!!!!!!N4h3ca(JSE%Di3!!!!!!!!! !!!!!!!!!!!!q!!-!r[m*!!B!!!!!!!!!!!!!!!%!!!!,!!!!!!!!!!!3!!!-!!! !!3!!!2lrrrm!!!!!#J!!!2rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr rrrrrrrrrrrrrrrrrrrrrrpbPD!"Ai!N%!!!!!'8!!!!!!!!!!!!!!!!$!!"T#3! !R"-!!!!!!!!!!!!!!!!!!!!!!!"T"J!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!$J!!DJ!!!!!1!!"U!!!!DJi!!!!!!!"U$J!!!!!!!'S1!!!!!!! !DJi!!!!!!!"U$J!!&!!!!*31!!!!!!!!P!i!!!!!!!#8$J!!!!!!!*31!!!!!!! !P!i!!!!!!!#8$J!!#J!!!*i1!!!+!!!!P!i!!!!!!!$E%J!!-3!!!+J1!!!!!!! !U!i!!!!!!!#S$J!!!!!!!+J1!!!!!!!!U!i!!!!!!!#S$J!!!!!!!+J1!!!!!!! !U!i!!!!!!!"+$`!!!J!!!%`2!!!!!!!!6!m!!!!!!!"-$`!!23!!!)N2!!#D!3! !)a%!!*S"!!#p%J!!(J!!!!`6!!"B!!!!C"-!!$J!!!$E%J!!!!!!!!!!!!!!!!! !!!!!!!!!!!"U$J!!!!!!!+J1!!!!!!!!!!!&!!B!!3!"!+J1!!!!!!!!U!i!!!! !!!!!!!!!!!!!!!!!!!!!!!!!U!i!!!!!!!#S$J!!!!!!!0X5!!!!!!!!U!i!!!! !!!"U$J!!!!!!!'S1!!!!!!!!U!i!!!!!!!!!!!!!!!!!!!!!!!!!!!!!U!i!!!! !!!#S$J!!!!!!!+J1!!!!!!!!U!i!!!!!!!#S$J!!!!!!!'S1!!!!!!!!U!i!!!! !!!"U$J!!!!!!!+J1!!!!!!!!5Jm!!!!!!!!!!!!!!!!!!+!#r'eGX,X"IJi!!!J !!!#'$J!!$J!!!'S1!!!!!!!!DJi!!!!!!!"U$J!!!!!!!'S1!!!!!!!!U!i!!!! !!!"+$`!!!!!!!+J1!!#L!!!!U!i!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!&*&8d9"8N0))&"28dP858p1)%&@38P-38*-45!0$3e ")("PFQeKEQ9ZG#"`Eh0TG'P[EL"TFb"KGQ&TE'&LE'8JBA3JG'KP)%4PF'&bG'e PER3JEfBJ6@9ND@0KE#"#D@p`D(PcD@0c,#"9E@AP)&9ZDACPFR0TG(NZ)&4SDA- JF'pcDA4TEfiJGfPXE#"LC5"cD'&bC@3JCA&eB@aXH5"LCA4hC@9Z)(4SC5"%CA" KFR4YC@jdFb"[CL"0C@4TBf&X)%*TEh"SHA0TBh-JB@jN)%pbCf&ZD@-J3fKPE@P cG(*j,L"8D'8JFh9MBf9cFfCeE#"MB@jND@4KG'8X)'%JCh*KC(9KG'9N)%j08L" cBfPPER4TFh3J+&"S,N3Z+5`JF(*PCQ9bB@*XH5"hDA4S)("[Fh3YC'pMG'pbB@` JCAK`CA*TC@jMC5`JGfPXE#"LC5"bCA0`EfjcD@*XC5"QEh)JG'KP)'eKEQ&RC@e PER3JEfBJD'PRD#"bCA0[E(9dD@pZ)%j08L"PFA9TF'ePER3X)'0[ER0TFh4TEQF JD@jTG'PKE'aj)'pQ)'%J3R*eDf9b)%45@$B`-#"dEb"LC5"TER0dB@aXC@3JD@i J4'9MC@eLCA)JEfBJG'KTFb"jC@&b)#Ja16Nf+5`JB@iJ38eB-L!e-$!JB@jN)'& Z)%&$8$)e-#"169)JFh"PBh4bEfePG'9b,L"8D'8JFh9MBf9cFfCeE#"MB@jND@4 KG'8JFfK[G@aN)'KKGQ8JCAKMC@aXC@jd)'9iF'9bD@9ZBf8JB@jN)'&Z)'PZG'9 bCA0d)'PZ)%j08L"YCA4SEf4[E'pRH5"KEQ3JCA&eDA"YC@jd,L"8D'8JFh9MBf9 cFfCeE#"MB@jND@4KG'8JGfPXE#"SBACP)(4SC5"[F("[FR4eEQPdH5"dEb"`CA* QEh*Y)'phEL"bCA0PBA*MD#"TEL"dD'8JCQPPE'3JEfBJBQP[E'pRD@0KE#"169) JB@jN,fpb)("KFR4TBfP`BA4P)'PZ)'pZCfpTEQFJBQP[E'pRD@0KE#"169)JF(* [DQ9MG(-JCQpMGA0TEQFJEfiJG'KP)(0dFR9MG(9bC5"NCA4PFQeTEQ&dD@pZ)'p Q)'*TEfa[CfPMB@`JE@pXC@0eE'9c,#"cG@0S)'&c)("PF(4TC'9c,#"`FQpdC@P ZFb"KEQ3JER9ME'9TBb"KBfPNFb`JB@jN)'pZ)(4SC5"cG(9NH5"[CL"dD'9TFL" TER4PFQ&MG'P[ER-X)'*j)(9cD@jR)%j08L"dC@0SEQPaG@9c,Jd09@ePj5"9EQP fCA*cDA4j)'&`F'aTCA-JD@jNDACTC(9KE#"cB@aKFRNYFf9dG'PZCbi0$8&`F'a TBf&dD@pZFb`JFA9[G'PZCb"dD'8JBA"`FQp`FQPKG'8JFQ9QCA*PEQ0P)'jeE@* PFL!S-c%c05da0M3h,6Nf+5"dEfGPG'KPFL"hDA4S)'%J3h9bFQPMG@aeE5"@DA4 KC5"KEQ3JG'KP)'jKE@9c)'&ZC#"KC'4bCA0cCA-JEfBJG(G[)("bEfCPFh0TEfj KE#"bC@CPFQ9PFb`JFfK[G@aN)(*PB@0S)(4SC5"5C@GTFh4bBA)X)&9YCH8J9@j TGQ9bFfPdH5`J8bdj-$%J1$FJ9@ePj5`J8hGPC'9Z,#"ZEh3JE'&dCA)JG'KKEL! 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!!!!!!!!!!!!!!!!!!!!"!!!!!YA0eC`Z'a#6P`J!+bcjVM!!!!#m!!!!#!!!!!% !!!")!!!!$`!!!&!!!!!%!!!!D!!!!!8!!!"`!!!!"J!!!(J!!!!,!!!!J!!!!"! !!!#)!!!!$!!!!*!!!!!!!J!!!13%!!!H!!!!$`!!!%ePC'PMD@jcDb",C@eT!!! $!!!!!$!!!!-!!!!,!!!!!`!!!!)!!!!,!!!!!!!!!!X!!!!!!!!!$"!!!!)!!!! H!!!!%J!!!&*&8d9"8N0))%914dP14895!!-!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!S"`!!!: --============_-1367822507==_============ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D Ingmar Sethson Dep. Organic Chemistry Ume=E5 University S-901 87 Ume=E5, Sweden E-mail: ingmar.sethson@chem.umu.se Ph. nr.: +46-90-16 62 86 =46ax. nr.: +46-90-13 88 85 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D --============_-1367822507==_============-- From owner-structural-nmr@net.bio.net Wed Oct 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!feed1.news.erols.com!netaxs.com!usenet From: Alan Engel Newsgroups: bionet.structural-nmr Subject: ERATO Positions in Japan Date: Thu, 03 Oct 1996 17:38:20 -0400 Organization: ISTA, Inc. Lines: 90 Message-ID: <3254324C.7D@netaxs.com> NNTP-Posting-Host: slip-113.netaxs.com Mime-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp; name="announcement.txt" Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b6 [ja] (WinNT; I) Content-Disposition: inline; filename="announcement.txt" ERATO GUIDE FOR PROSPECTIVE RESEARCHERS - 1996 Link - http://www2.jst-c.go.jp/jst/erato/erato-e/contents-e.html JAPAN SCIENCE AND TECHNOLOGY CORPORATION Link - http://www.jst-c.go.jp/EN/ INTRODUCTION TO ERATO Link - http://www2.jst-c.go.jp/jst/erato/erato-e/NewPositions/Introduction.html The Japan Science and Technology Corporation (JST) (formerly the Research Development Corporation of Japan), a statutory agency of the Japanese Government, invites applications for research positions in its new ERATO projects listed below from young scientists interested in recognized, well-funded, multidisciplinary research. ERATO projects operate for five-year terms and are independent from the Project Directors home institutions. The U.S. National Science Foundation's JTEC Program (see http://itri.loyola.edu) found: The quality of science in ERATO is "uniformly high." The research is "cutting edge." In a number of (past) projects, ERATO was responsible for expanding work that was in its infancy, to that it had international impact." Work from ERATO is "renowned worldwide." "Numerous projects are 'world class'". "In at least one instance, the ERATO Project can be considered to have created the field." Kawato DYNAMIC BRAIN Project Link - http://www2.jst-c.go.jp/jst/erato/erato-e/NewPositions/Kawato.html" Fields: ROBOTICS, NEUROPHYSIOLOGY, ELECTROPHYSIOLOGY, COMPUTATIONAL THEORY, ARTIFICIAL INTELLIGENCE Research: Neurophysiological events involved in training the brain, especially the cerebellum to control motor skills, including implementation of theories in robots Director: Dr. Mitsuo Kawato, ATR Inoue PHOTOCHIROGENESIS Project Link - http://www2.jst-c.go.jp/jst/erato/erato-e/NewPositions/Inoue.html Fields: PHOTOCHEMISTRY, ORGANIC CHEMISTRY, PHYSICAL CHEMISTRY, SUPRAMOLECULAR CHEMISTRY, LASER CHEMISTRY Research: Creation of chiral compounds using circularly polarized light, including circularly polarized VUV light, chiral photosensitizers and chiral hosts Director: Professor Yoshihisa Inoue, Osaka University Yokoyama CYTOLOGIC Project Link - http://www2.jst-c.go.jp/jst/erato/erato-e/NewPositions/Yokoyama.html Fields: BIOCHEMISTRY, MOLECULAR BIOLOGY, COMPUTING THEORY, STRUCTURAL BIOLOGY Research: Amino acyl-tRNA synthetases as keys to altering the genetic code and elucidating the autocompiling responses of cells to their environment Director: Professor Shigeyuki Yokoyama, The University of Tokyo Tsukita CELL AXIS Project Link - http://www2.jst-c.go.jp/jst/erato/erato-e/NewPositions/Tsukita.html Fields: CELL BIOLOGY, MOLECULAR BIOLOGY, NEUROPHYSIOLOGY, MEMBRANE BIOLOGY, BIOCHEMISTRY Research: The mechanisms by which cells arrange their internal structures in response to their environment, emphasis on epithelial and nerve cells Director: Professor Shoichiro Tsukita, Kyoto University Joining ERATO from OVERSEAS Link - http://www2.jst-c.go.jp/jst/erato/erato-e/NewPositions/JoiningERATO.html Deadline - 1 February 1997 The 1996 ERATO GUIDE FOR PROSPECTIVE RESEARCHERS is available on the Internet (http://www2.jst-c.go.jp/jst/erato/erato-e/NewPositions/) or from the ERATO Overseas Representative. Applicants must hold a Ph.D. or equivalent degree with less than 5 years of postdoctoral experience, be willing to stay at least one year, and be fluent in English or Japanese. Applications must include 1) a letter describing background and interests (important!), 2) curriculum vitae, 3) list of publications, 4) copies of representative publications, and 5) names and addresses of references. SEND APPLICATIONS BY POST (SNAIL MAIL) ONLY. APPLICATIONS BY ELECTRONIC MAIL CANNOT BE ACCEPTED. For an ERATO APPLICATION FORM See - http://www2.jst-c.go.jp/jst/erato/erato-e/NewPositions/Form.txt Applications Accepted by ERATO Overseas Representative, c/o, ISTA, Inc. 950 Conestoga Road, Rosemont, PA 19010 USA Voice: +1-610-527-4538, Fax: +1-610-527-2041 Internet: engel@jrdc.go.jp From owner-structural-nmr@net.bio.net Wed Oct 02 23:00:00 1996 Path: biosci!CARIBE.CHEM.UKY.EDU!cammers From: cammers@CARIBE.CHEM.UKY.EDU (Arthur Cammers) Newsgroups: bionet.structural-nmr Subject: Re: Solubilizing proteins Date: 3 Oct 1996 04:19:15 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 32 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <"13435120016991.149557.MRX*"@MHS> NNTP-Posting-Host: net.bio.net > >We have a 12kDa cytoplasmic protein which is insoluble in >aqueous media at NMR concentrations, we would prefer a MINIMUM >of 1 mmol in 0.5 ml. > >We thought about using a percentage of trifluoroethanol ( TFE >), but this appears to have a "side-effect" of instilling >alpha-helical structure in unstructured loops and bends. Our >protein is about 90% alpha-helical already in four bundles >connected by loops. Any more helicity and we will lose >tertiary structure and end up with a helical rod !! Not good. Did you observe more helical structure upon addition of TFE? I would really be surprised if this were the case. It seems to me that you can be fairly confident that small amounts of TFE (10-15mol%) would not affect the structure of you protein much compared to the water structure and may confer the solubility you desire. TFE does not enforce helical structure. You will not get that helical rod. TFE appears to stabilize helical propensity only in segments of polypeptide that are prone toward helicity. There have even been reports of TFE stabilizing sheets in some sequences. Hexafluoroisopropanol is an option as is DMSO. Arthur Cammers-Goodwin Assistant Professor of Chemistry Department of Chemistry-Organic Division University of Kentucky acgood1@pop.uky.edu http://www.chem.uky.edu/research/cammers/cammerscv.html From owner-structural-nmr@net.bio.net Thu Oct 03 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!news-peer.gsl.net!news.gsl.net!news-hk.gsl.net!news.gsl.net!newsgate.cuhk.edu.hk!hpg30a.csc.cuhk.hk!news.cuhk.edu.hk!sunrise.pku.edu.cn!csb0!owner From: owner@csb0 (Wang Arthur) Newsgroups: bionet.structural-nmr Subject: welcome to sbl Date: 4 Oct 1996 02:16:59 GMT Organization: Peking Univerity Lines: 49 Message-ID: <531s2r$dna@sunrise.pku.edu.cn> NNTP-Posting-Host: csb0.ipc.pku.edu.cn X-Newsreader: TIN [version 1.2 PL1] ********** Welcome to the Structural Biology List! ********** Structural biology has already drawn much attention: it opens the door to a new era of biology. We announce here that a mailing list for structural biologists has been created. It will bring biologists/chemists/pharmacists all across the globe together to a new electronic frontier. The list server locates at the Institute of Physical Chemistry, Peking University, Beijing, China. We send this mail to invite your membership. The suggested topics of this mailing list include: o Macromolecular crystallography o NMR and other spectroscopies o Molecular modeling and design o Structure-based drug design and QSAR o Bioinformatics o Theoretical and computational biology To subscribe, you only need to send a short mail to owner@ipc.pku.edu.cn like this, "please add me to the SBL ..." while stating your name, title, e-mail, address, country and academic interests. Or you can save your time by filling out the following form and send it back to owner@ipc.pku.edu.cn. No fee and no restriction to subscribe. --------------- Structural Biology Mailing List -------------- ---------------------- Membership Form ---------------------- Name: Title: Address: Country: E-mail: Academic interests: -------------------------------------------------------------- Please forward this message to your friends as many as possible. Thank you for concern. Prof. Luhua Lai Institute of Physical Chemistry Peking University, Beijing, P.R.China From owner-structural-nmr@net.bio.net Thu Oct 03 23:00:00 1996 Path: biosci!CSB0.IPC.PKU.EDU.CN!owner From: owner@CSB0.IPC.PKU.EDU.CN (Lists Owner) Newsgroups: bionet.structural-nmr Subject: welcome to sbl Date: 3 Oct 1996 20:33:41 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 49 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net ********** Welcome to the Structural Biology List! ********** Structural biology has already drawn much attention: it opens the door to a new era of biology. We announce here that a mailing list for structural biologists has been created. It will bring biologists/chemists/pharmacists all across the globe together to a new electronic frontier. The list server locates at the Institute of Physical Chemistry, Peking University, Beijing, China. We send this mail to invite your membership. The suggested topics of this mailing list include: o Macromolecular crystallography o NMR and other spectroscopies o Molecular modeling and design o Structure-based drug design and QSAR o Bioinformatics o Theoretical and computational biology To subscribe, you only need to send a short mail to owner@ipc.pku.edu.cn like this, "please add me to the SBL ..." while stating your name, title, e-mail, address, country and academic interests. Or you can save your time by filling out the following form and send it back to owner@ipc.pku.edu.cn. No fee and no restriction to subscribe. --------------- Structural Biology Mailing List -------------- ---------------------- Membership Form ---------------------- Name: Title: Address: Country: E-mail: Academic interests: -------------------------------------------------------------- Please forward this message to your friends as many as possible. Thank you for concern. Prof. Luhua Lai Institute of Physical Chemistry Peking University, Beijing, P.R.China From owner-structural-nmr@net.bio.net Thu Oct 03 23:00:00 1996 Path: biosci!faseb.org!cpk-news-feed1.bbnplanet.com!cpk-news-feed2.bbnplanet.com!nntp-hub2.barrnet.net!news.sgi.com!howland.erols.net!EU.net!chsun!news.eunet.ch!usenet From: Reto Koradi Newsgroups: bionet.structural-nmr Subject: Re: x-Term on PC for uxnmr? Date: Fri, 04 Oct 1996 18:46:19 +0200 Organization: Spectrospin AG Lines: 17 Message-ID: <32553F5B.41C6@spectrospin.ch> References: <325517D9.167E@biochem.mpg.de> NNTP-Posting-Host: birchwil.spectrospin.ch Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP12) To: Rudolf Kinder Rudolf Kinder wrote: > Does anyone know how to run uxnmr on a PC (windows NT)? > Is it pssible to run uxnmr in an x-terminal? UXNMR on an X32? No, that can't work. The X32 has a proprietary graphics library, which does not work over a network, and is not supported by anybody else. XWIN-NMR should be able to display to an X terminal. For display on a PC, you would need an X server. I'm not sure what Bruker officially recommends there, one that seems to be popular is Exceed (http://www.hummingbird.com). Bruker also sells NMR software for PCs, contact your local sales office for information. -- Reto Koradi (kor@mol.biol.ethz.ch, http://www.mol.biol.ethz.ch/~kor) From owner-structural-nmr@net.bio.net Thu Oct 03 23:00:00 1996 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!news.ycc.yale.edu!news From: "Axel T. Brunger" Newsgroups: bionet.structural-nmr Subject: patch for X-PLOR(online) 3.843, beta-release Date: Fri, 04 Oct 1996 12:18:38 -0400 Organization: Howard Hughes Medical Institute Lines: 44 Message-ID: <325538DE.63DE@laplace.csb.yale.edu> NNTP-Posting-Host: wilson.csb.yale.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP22) ------------------------------------------------------------- First, I would like to make a general remark: the current distribution of X-PLOR(online) is a beta-release and not yet complete. I would very much appreciate any comments and suggestions you have. ------------------------------------------------------------- Second, there is a new patch for X-PLOR(online) 3.843: patch3843c replaces the following files: $XPLOR/tutorial/xtalrefine/*.inp $XPLOR/tutorial/xtal_maps/*.inp $XPLOR/tutorial/xtal_torsion/*.inp $XPLOR/tutorial/xtal_analysis/*.inp $XPLOR/tutorial/xtal_waterpick/*.inp Changes: NEW: Examples for NCS restraints or constraints are included. NEW: Fast nonbonded interaction list generation is included. Option for fixed atoms is included (was already in patch3843a) Atoms that are not included in the refinement are kept fixed (was already in patch3843a). This patch is available on the X-PLOR(online) server. It doesn't require recompilation. Just replace the tutorial files. We'll remove patch3843a because patch3843c overwrites the previous patch. Axel Brunger -- ======================================================================= | Axel T. Brunger Dept. Molecular Biophysics and Biochemistry| | Professor/Investigator Bass Center, 266 Whitney Avenue | | Office: 203-432-6143 Howard Hughes Medical Institute/Yale Univ. | | FAX: 203-432-6946 New Haven, CT 06520, USA. | | http://xplor.csb.yale.edu/~brunger | | mailto://brunger@laplace.csb.yale.edu | ======================================================================= From owner-structural-nmr@net.bio.net Thu Oct 03 23:00:00 1996 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!in1.uu.net!fu-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!usenet From: Rudolf Kinder Newsgroups: bionet.structural-nmr Subject: x-Term on PC for uxnmr? Date: Fri, 04 Oct 1996 14:57:45 +0100 Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 7 Message-ID: <325517D9.167E@biochem.mpg.de> NNTP-Posting-Host: acca.biochem.mpg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) Does anyone know how to run uxnmr on a PC (windows NT)? Is it pssible to run uxnmr in an x-terminal? Thanks Rudolf kinder kinder@biochem.mpg.de From owner-structural-nmr@net.bio.net Thu Oct 03 23:00:00 1996 Path: biosci!agate!spool.mu.edu!howland.erols.net!news-peer.gsl.net!news.gsl.net!portc01.blue.aol.com!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: blackorb@aol.com (Black Orb) Newsgroups: bionet.structural-nmr Subject: Question dealing with organismal biology Date: 4 Oct 1996 00:22:45 -0400 Organization: America Online, Inc. (1-800-827-6364) Lines: 7 Sender: root@newsbf02.news.aol.com Message-ID: <5323el$qun@newsbf02.news.aol.com> Reply-To: blackorb@aol.com (Black Orb) NNTP-Posting-Host: newsbf02.mail.aol.com I need some help with this question I got from my biology professor: - Why do ribosomes appear to be the first membrane bound organelle that developed in procaryotic cells? I don't quite know how to begin, but any help would be appreciated!! From owner-structural-nmr@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!howland.erols.net!EU.net!Belgium.EU.net!news From: Guy Cotton, LSD Newsgroups: bionet.structural-nmr Subject: Gamma rays and sterilisation (B) Date: 7 Oct 1996 22:03:37 GMT Organization: EUnet Belgium, Leuven, Belgium Lines: 25 Message-ID: <53bunp$th@news2.Belgium.EU.net> NNTP-Posting-Host: dialup11.liege.eunet.be Gamma rays and sterilisation (B) -------------------------------- I'm a dental surgeon and I send again this mail. I hope I will receive more answers and more precisions. I want to ask to the Specialists some questions: are the Gamma rays sterilize all the bacteriae and viruses ? One application is the Gamma's use for dental implants who are inserted in the maxillary bones. Do you think that Gamma rays will give all securities about sterilization? Wich dose will be like the best ? And this dose during how many time ? I hope you will give fundamental answers and all references as possible who will confirm the real effects of the Gamma rays. Please, answer on my private E-mail, undermentioned. Thank you very much and have a good day! Guy Cotton, LSD. (from Liege, in Belgium) Any question or suggestion or opinion will be appreciated on the SMTP From owner-structural-nmr@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: "Simon M. Brocklehurst" Newsgroups: bionet.structural-nmr Subject: NAOMI - Important messages Date: Mon, 07 Oct 1996 09:42:34 +0100 Organization: University of Oxford Lines: 65 Message-ID: <3258C27A.15FB7483@bioch.ox.ac.uk> NNTP-Posting-Host: nmrv.ocms.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 4.1.3_U1 sun4m) NAOMI - Important messages to all users - please read. _____________________________________________________________________________ **** The NAOMI anonymous FTP server is now back up again after some considerable downtime. Sorry for all the inconvenience this caused. ----------------------------------------------------------------------------- **** I've taken this opportunity to make available the Version 3.0 User Guide which is complete reworking of the old User Guide. It is much improved (fast loading, better organised etc). It is available only on the Web site (select the User Guide - Europe link) at present. NAOMI Web site URL given below. Version 3.0 of the program is not yet available (release soon), but the new User Guide is applicable to the current version. ----------------------------------------------------------------------------- **** Due to bandwidth problems, especially across the Atlantic and to the Pacific Rim, I'm looking for places that would be prepared to act as mirror sites for the NAOMI distribution (you need an anonymous ftp server to do this). If you are interested in doing this, please e-mail me at: smb@bioch.ox.ac.uk ------------------------------------------------------------------------------ ****** What is NAOMI ? ******************* NAOMI is a computer program system for studying 3-D structures of proteins. NAOMI is available free of charge for academic users. NAOMI Version 2.4c is available as of now from the NAOMI Web site at: http://www.ocms.ox.ac.uk/~smb/Software/N_details/naomi.html or via anonymous ftp ftp://nmrz.ocms.ox.ac.uk/pub/smb/naomi i.e. at nmrz.ocms.ox.ac.uk in directory pub/smb/naomi/ _____________________________________________________________________________ | | ,_ o Simon M. Brocklehurst, | / //\, Oxford Centre for Molecular Sciences, Department of Biochemistry, | \>> | University of Oxford, Oxford, UK. | \\, E-mail: smb@bioch.ox.ac.uk | WWW: http://www.ocms.ox.ac.uk/~smb/ |____________________________________________________________________________ From owner-structural-nmr@net.bio.net Mon Oct 07 23:00:00 1996 Path: biosci!MAILBOX.SYR.EDU!lpappala From: lpappala@MAILBOX.SYR.EDU (Lucia Pappalardo) Newsgroups: bionet.structural-nmr Subject: Xwin-nmr to NMR Triad Date: 8 Oct 1996 15:49:24 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear netters, does anyone know if is possible to convert files processed with Xwin-nmr to NMR Triad format? Thanks in advance Lucia From owner-structural-nmr@net.bio.net Tue Oct 08 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.sgi.com!howland.erols.net!www.nntp.primenet.com!nntp.primenet.com!arclight.uoregon.edu!news.ibm.net.il!newsfeed.uk.ibm.net!02-newsfeed.univie.ac.at!03-newsfeed.univie.ac.at!mail.boku.ac.at!news From: Iain Wilson Newsgroups: bionet.structural-nmr Subject: Glycoscience Network Live! Date: Wed, 09 Oct 1996 19:02:47 +0200 Organization: Universität für Bodenkultur Wien Lines: 43 Message-ID: <325BDAB7.80C@edv1.boku.ac.at> Reply-To: wilson@edv1.boku.ac.at NNTP-Posting-Host: 141.244.231.42 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I) Glycoscience Network Live! We are pleased to announce the release of the Glycoscience Network Live! service for members of The Glycoscience Network (TGN) community. This service consists of a WWW-based scientific resource in which TGN members may access an interactive environment on a continuous basis to participate in online scientific events including lectures, discussions, poster sessions, journal clubs, collaborative scientific projects, structural and informatic resources, glossary, other scientific projects, and a Job and Trade Centre. These activities will be available on a year-round basis to subscribed TGN members. As a starting point the interactive facility and material for The Second Electronic Glycoscience Conference (EGC-2, http://bellatrix.pcl.ox.ac.uk/egc2/) is available through the service. EGC-2 registrants will receive one year's free membership to TGN and its services starting from October 1 1996. For others membership may be obtained for a subscription equivalent to the EGC-2 registration fee via the registration facility through TGN's page at: http://bellatrix.pcl.ox.ac.uk/TGN/ Membership fee for one year is 35 pounds (50 dollars) with a reduced rate of 20 pounds (30 dollars) for students. These fees will aid in the support and improvement of services and connections to TGN members. The Glycoscience Network Live! service is currently available via http://bellatrix.pcl.ox.ac.uk:8000/. A US mirror service and other server service upgrades will be released in due course. We encourage TGN members to participate in projects and will endeavour to support member contributions via available technical and financial means. We offer an open invitation to members to submit their interests and project suggestions for consideration to egc2org@bellatrix.pcl.ox.ac.uk TGN and the Glycoscience Network Live! service will be provided by Greenlea Communications which is dedicated to the establishment of high quality virtual environments and resources for the scientific community. Barry J. Hardy, barry@bellatrix.pcl.ox.ac.uk and Iain B. H. Wilson, wilson@edv1.boku.ac.at From owner-structural-nmr@net.bio.net Tue Oct 08 23:00:00 1996 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: 99Ru Date: 9 Oct 1996 10:44:21 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Netters, I am looking for an NMR lab in the East Cost (the closer to Princeton the better) which would have capacity for, and interest in runnig a couple of 1D 99Ru experiments for us. Thanks in advance, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry, Frick Lab., ph# (609) 258 2342 Washington Road fax# (609) 258 6746 Princeton, NJ 08544, USA From owner-structural-nmr@net.bio.net Sun Oct 13 23:00:00 1996 Path: biosci!chbs.ciba.com!bstark From: bstark@chbs.ciba.com (Wilhelm Stark) Newsgroups: bionet.structural-nmr Subject: FRED Software Date: 14 Oct 1996 03:01:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: <199610141101.MAA13979@bionmr2.nmr.fd.chbs> NNTP-Posting-Host: net.bio.net Dear str-nmr readers, We are using the FRED-Software to analyze INADEQUATE spectra in a Varian environment. We are now facing the necessity to process also spectra from a Bruker instrument. The FRED software has the option of processing data in the Bruker aspect format. Our data, however, are in the UXNMR format. Who has experience in processing UXNMR data with the FRED software? Please reply directly to: Hanspeter Sauter, Ciba-Geigy, Basel, Switzerland xfosh@chbs.ciba.com %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% * * c Dr. Wilhelm Stark Tel.: +41 61 697 93 43 c * Ciba-Geigy AG +41 61 697 24 05 * i Physics Departement +41 61 697 79 74 i * Bio-NMR * b R-1055.5.26 Fax.: +41 61 697 37 04 b * Postfach * a CH-4002 BASEL Email: BSTARK@CHBS.CIBA.COM a * Switzerland * * * %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From owner-structural-nmr@net.bio.net Mon Oct 14 23:00:00 1996 Path: biosci!agate!spool.mu.edu!howland.erols.net!newsfeed.internetmci.com!in1.uu.net!EU.net!Austria.EU.net!01-newsfeed.univie.ac.at!swidir.switch.ch!scsing.switch.ch!elna.ethz.ch!usenet From: Peter Guentert Newsgroups: bionet.structural-nmr Subject: DIANA is now DYANA! Date: Tue, 15 Oct 1996 13:11:48 +0100 Organization: Swiss Federal Institute of Technology (ETHZ) Lines: 32 Message-ID: <32637F84.49FC@mol.biol.ethz.ch> NNTP-Posting-Host: baldur.ethz.ch Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; SunOS 5.4 sun4m) The program DIANA for NMR structure calculation has been replaced by our new program DYANA "Dynamics Algorithm for NMR Applications" -- - - - that provides all functionality of its predecessor and many extensions, in particular: - torsion angle dynamics for highly efficient structure calculation - optimal parallelization on multiprocessor systems - a powerful command language combining ease-of-use and flexibility, including a set of macros to perform routine tasks Compiled versions of DYANA for a variety of Unix computer systems (SGI, DEC, Cray, IBM, Sun, Convex) are available free of charge to all users. For further information about DYANA and on how to download and install the software, please have a look at the DYANA home page: http://www.mol.biol.ethz.ch/wuthrich/software/dyana/ Peter Guentert ---------------------------------------------------------------------- Dr. Peter Guentert phone +41 1 633 34 54 Institut fuer Molekularbiologie & Biophysik fax +41 1 633 11 51 ETH-Hoenggerberg, HPM G22 guentert@mol.biol.ethz.ch CH-8093 Zuerich (Switzerland) http://www.mol.biol.ethz.ch/~guentert ---------------------------------------------------------------------- From owner-structural-nmr@net.bio.net Wed Oct 16 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!newsfeed.internetmci.com!btnet!btnet-feed1!theplanet.net!news From: "Michael Bernstein" Newsgroups: bionet.structural-nmr Subject: Spectral Browser Date: 16 Oct 1996 17:07:47 GMT Organization: ASTRA Charnwood Lines: 19 Message-ID: <01bbbb84$afd0e240$8e4698c2@bytb6x1u> NNTP-Posting-Host: b43.modem.planet.internet.co.uk X-Newsreader: Microsoft Internet News 4.70.1155 Hi I'm looking to use an application to view NMR spectra. This might be done within a Web browser. To this end, I heard about an MRI image viewing applet (any details?), and a project from the OMF (Spectral Browser - still alpha release). My needs really are simple: our lab produces a large number of routine spectra (on Varian instruments), and the chemists would like to view their spectra, play around with expansions, measure J's, plot, etc. I know there's some good PC-based processing software out there, but my customers want something easy (and idiotproof ;-)) I'd be interested in your thoughts on this... Thanks, Mike ASTRA Charnwood michael.bernstein@charnwood.gb.astra.com From owner-structural-nmr@net.bio.net Thu Oct 17 23:00:00 1996 Path: biosci!OLIGO.UTMB.EDU!quyx From: quyx@OLIGO.UTMB.EDU (You Xing Qu) Newsgroups: bionet.structural-nmr Subject: saturation transfer Date: 18 Oct 1996 12:27:37 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <199610181953.OAA08005@oligo.utmb.edu> NNTP-Posting-Host: net.bio.net Dear netters, I want to measure H/H exchange rate between peptide amide proton and water. Normally people use continuous preirradiation to saturate water. I wish to know if there is any literature where pulsed field gradients (PFG) is used for saturation transfer measurements or some people have worked on this. Any help and suggestion is highly appreciated. Thanks a lot in advance, Youxing. Youxing Qu Dept. of Human Biological Chem. & Genetics Univ. of Texas Medical Branch at Galveston Galveston, TX 77555-1052, USA E-mail: quyx@oligo.utmb.edu From owner-structural-nmr@net.bio.net Fri Oct 18 23:00:00 1996 Path: biosci!bloom-beacon.mit.edu!howland.erols.net!EU.net!uunet!news-in2.uu.net!ulowell.uml.edu!news.cs.umb.edu!oitnews.harvard.edu!purdue!news.bu.edu!svsgi!vajda From: vajda@svsgi.bu.edu (Sandor Vajda) Newsgroups: bionet.structural-nmr Subject: postdoctoral positions available for protein modeller Date: 18 Oct 1996 21:42:37 GMT Organization: Boston University Lines: 9 Message-ID: <548tkd$6u7@news.bu.edu> NNTP-Posting-Host: svsgi.bu.edu X-Newsreader: TIN [version 1.2 PL2] Postdoctoral positions are available in computational chemistry and protein modeling. Research focuses on algorithm and program development in the following areas (1) protein structure prediction by homologous extension; and (2) docking and binding free energy evaluation. Please send CV, and names and telephone numbers of 3 references to: S. Vajda, Department of Biomedical Engineering, Boston University, 44 Cummington St., Boston MA 02215. Phone: 617-353-4757, FAX: 617-353-6766, e-mail: vajda@enga.bu.edu From owner-structural-nmr@net.bio.net Fri Oct 18 23:00:00 1996 Path: biosci!biosci!not-for-mail From: zhiping@engpub6.bu.edu (Zhiping Weng) Newsgroups: bionet.general,bionet.molbio.proteins,bionet.xtallography,bionet.structural-nmr,bionet.molec-model Subject: postdoctoral position available for molecular modeling Date: 19 Oct 1996 12:44:21 -0700 Organization: Boston University Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <546v0d$12e@news.bu.edu> NNTP-Posting-Host: net.bio.net Keywords: homologous modeling, docking, binding free energy calculation Xref: biosci bionet.general:23681 bionet.molbio.proteins:9063 bionet.xtallography:2950 bionet.structural-nmr:1560 bionet.molec-model:1192 Postdoctoral positions are available in computational chemistry and protein modeling. Research focuses on algorithm and program development in the following areas (1) protein structure prediction by homologous extension; and (2) docking and binding free energy evaluation. Please send CV, and names and telephone numbers of 3 references to: S. Vajda, Department of Biomedical Engineering, Boston University, 44 Cummington St., Boston MA 02215. Phone: 617-353-4757, FAX: 617-353-6766, e-mail: vajda@enga.bu.edu From owner-structural-nmr@net.bio.net Sat Oct 19 23:00:00 1996 Path: biosci!agate!howland.erols.net!news-peer.gsl.net!news.gsl.net!news-stock.gsl.net!news.gsl.net!snunews.snu.ac.kr!usenet From: "Lee, Ji Hyun" Newsgroups: bionet.structural-nmr Subject: Reference for 'model free appoach' Date: Sun, 20 Oct 1996 14:44:34 +0900 Organization: College of Pharmacy, Seoul National University Lines: 18 Message-ID: <3269BC42.2104@plaza.snu.ac.kr> Reply-To: newera@plaza.snu.ac.kr NNTP-Posting-Host: 147.46.8.60 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-2 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) Although I'd like to understand 'model free approach', I deeply feel my lack of theoretical background. I've an original paper on it from Journal of Ameirican Cheimcal Society which of course comes to my sense vaguely. 1. What text or review could lead me to understand it? Both essential digest or comprehensive review are helpful to me. Using 'Model free approach' I expect to obtain order parameters and can analyze dynamic motion of my protein in solution which is N15, C13 uniformly labelled. 2. If I get order parameters of all the carbon atoms by C13-NMR, for refinement (e.g. 'IRMA(Iterative Relxation Matrix Approach') can I apply it to back calculate NOE peak from simmulated annealed structures? Any comment on above either will be appreciated. Thanks... From owner-structural-nmr@net.bio.net Sat Oct 19 23:00:00 1996 Path: biosci!agate!usenet.kornet.nm.kr!snunews.snu.ac.kr!usenet From: "Lee, Ji Hyun" Newsgroups: bionet.structural-nmr Subject: Reference for NMR data processing? Date: Sun, 20 Oct 1996 14:58:37 +0900 Organization: College of Pharmacy, Seoul National University Lines: 13 Message-ID: <3269BF8D.1FDF@plaza.snu.ac.kr> Reply-To: newera@plaza.snu.ac.kr NNTP-Posting-Host: 147.46.8.60 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-2 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) I'm learning NMR data processing for myself such as window function, linear prediction, discrete fourier transfrom, zero filling, etc. So I'm looking for books, papers, or reviews pertinent to the subject. Both essential digests and comprehensive references are much helpful to me. I'm trying to use NMRpipe or Felix. I've read 'modern NMR techniques for chemistry research, Derome', 'NMR of proteins and nucleic acids, Wutrich'. I'm measuring several NMR spectra of my protein, whose molecular weight is 5.5 kd (11 kd in dimer state) : 13C-1H HSQC, 2D homonuclear NOESY, 3D 1H-13C-1H NOESY-HSQC, 3D 1H-15N-1H NOESY-HSQC, 2D HMQC-J and some triple resonance(CBCA(CO)NH, CBCANH, gradient version of HCCH-TOCSY). I'll appreciate any comments about processing. Thanks. From owner-structural-nmr@net.bio.net Sun Oct 20 23:00:00 1996 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: Reference for 'model free appoach' Date: 21 Oct 1996 10:40:46 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 52 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <3269BC42.2104@plaza.snu.ac.kr> NNTP-Posting-Host: net.bio.net Dear Lee, Let me extend Alexandre's comments with the following two books you probably wanted to look at: NMR of Proteins (Eds.: G. M. Clore and A. M. Gronenborn), CRC Press, 1993. NMR in Drug Design (Ed.: D. J. Craik), CRC Press, 1996. I would recommend to take a look at the following review, too: James, T. L., Computational strategies pertinent to NMR solution structure determination Current Opinion in Structural Biology, 4, 275-284, 1994. Best wishes, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry, Frick Lab., ph# (609) 258 2342 Washington Road fax# (609) 258 6746 Princeton, NJ 08544, USA On Sun, 20 Oct 1996, Lee, Ji Hyun wrote: > Although I'd like to understand 'model free approach', I deeply feel my > lack of theoretical background. I've an original paper on it from > Journal of Ameirican Cheimcal Society which of course comes to my sense > vaguely. > > 1. What text or review could lead me to understand it? Both essential > digest or comprehensive review are helpful to me. > Using 'Model free approach' I expect to obtain order parameters and can > analyze dynamic motion of my protein in solution which is N15, C13 > uniformly labelled. > > 2. If I get order parameters of all the carbon atoms by C13-NMR, for > refinement (e.g. 'IRMA(Iterative Relxation Matrix Approach') can I apply > it to back calculate NOE peak from simmulated annealed structures? > > Any comment on above either will be appreciated. > > Thanks... > > From owner-structural-nmr@net.bio.net Sun Oct 20 23:00:00 1996 Path: biosci!igc.phys.chem.ethz.ch!abonvin From: abonvin@igc.phys.chem.ethz.ch (abonvin) Newsgroups: bionet.structural-nmr Subject: Re: Reference for 'model free appoach' Date: 21 Oct 1996 01:12:35 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: <199610210809.JAA01040@shiraz.ethz.ch> References: <3269BC42.2104@plaza.snu.ac.kr> NNTP-Posting-Host: net.bio.net >1. What text or review could lead me to understand it? Both essential >digest or comprehensive review are helpful to me. >Using 'Model free approach' I expect to obtain order parameters and can >analyze dynamic motion of my protein in solution which is N15, C13 >uniformly labelled. The two basic references are the one you mentionned: JACS 104, 4546 (1982) and JACS 104, 4559 (1882). If you are looking at a description of how to interpret your relaxation data and extract order parameters, there are lots of references, but one of my favorite because of it's clarity is: Li & Montelione, Biochemistry 34, 2408 (1995). >2. If I get order parameters of all the carbon atoms by C13-NMR, for >refinement (e.g. 'IRMA(Iterative Relxation Matrix Approach') can I apply >it to back calculate NOE peak from simmulated annealed structures? Yes, but ideally you would need order parameters for each proton pair, which is of course unpossible experimentaly. You could use your C13 order parameters as "residue order parameter" and define some combination rule for interresidue interactions. I am however not convinced that this will give you a much better correspondence between your back-calculated and experimental NOEs. If you want to use order parameters in your back-calculations you should have them for all relevant interactions. Better ignore them than introduce them for only part of your data. And since you mentionned it, IRMA allows the input of order parameters, as a pairlist (i.e. for each proton pair). For info on IRMA check the Kaptein's group: http://www-nmr.chem.ruu.nl Cheers, Alexandre ========================================================================== | Dr. Alexandre Bonvin | Phone: Int+41-1-632-5504 | | Physical Chemistry, ETHZ | Fax: Int+41-1-632-1039 | | Universitatstrasse 6 | Email: abonvin@igc.phys.chem.ethz.ch | | 8092 Zurich, Switzerland | http://igc.chem.ethz.ch/abonvin | ========================================================================== From owner-structural-nmr@net.bio.net Sun Oct 20 23:00:00 1996 Path: biosci!PHOENIX.PRINCETON.EDU!ipelczer From: ipelczer@PHOENIX.PRINCETON.EDU (Istvan Pelczer) Newsgroups: bionet.structural-nmr Subject: Re: Reference for NMR data processing? Date: 21 Oct 1996 10:31:00 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 56 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <3269BF8D.1FDF@plaza.snu.ac.kr> NNTP-Posting-Host: net.bio.net Dear Lee, We have published a review with Sandor Szalma few years ago, which still could be a good source of relevant information: Pelczer, I., and Szalma, S.; Multidimensional NMR and Data Processing Chem. Rev., 91(7), 1507-1524, 1991. An update is in press: Pelczer, I., and Carter, B. G., Data processing in multidimensional NMR Chapter for: "Protein NMR Protocols" in: "Methods in Molecular Biology", Ed.: D. G. Reid Humana Press, NJ (ISBN 0-89603-309-0) (Humana Press: humana@interramp.com, or http://lbin.com/humana.html -- with direct ordering available) Besides the references in these publications I can recommend W. R. Croasmun and R. M. K. Carlson's excellent book (Two-Dimensional NMR Spectroscopy, Second Edition(!), VCH Publishers, Inc., 1994) which has great Chapters you'll benefit of. All the best, Istvan wwww,wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Istvan Pelczer, Ph.D. Email: ipelczer@princeton.edu Senior NMR Spectroscopist Princeton University Department of Chemistry, Frick Lab., ph# (609) 258 2342 Washington Road fax# (609) 258 6746 Princeton, NJ 08544, USA On Sun, 20 Oct 1996, Lee, Ji Hyun wrote: > I'm learning NMR data processing for myself such as window function, > linear prediction, discrete fourier transfrom, zero filling, etc. So I'm > looking for books, papers, or reviews pertinent to the subject. Both > essential digests and comprehensive references are much helpful to me. > I'm trying to use NMRpipe or Felix. I've read 'modern NMR techniques for > chemistry research, Derome', 'NMR of proteins and nucleic acids, > Wutrich'. > I'm measuring several NMR spectra of my protein, whose molecular weight > is 5.5 kd (11 kd in dimer state) : 13C-1H HSQC, 2D homonuclear NOESY, 3D > 1H-13C-1H NOESY-HSQC, 3D 1H-15N-1H NOESY-HSQC, 2D HMQC-J and some triple > resonance(CBCA(CO)NH, CBCANH, gradient version of HCCH-TOCSY). > I'll appreciate any comments about processing. > Thanks. > > From owner-structural-nmr@net.bio.net Mon Oct 21 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.structural-nmr Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 22 Oct 1996 02:59:12 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199610220901.CAA28802@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-structural-nmr@net.bio.net Mon Oct 21 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!howland.erols.net!vixen.cso.uiuc.edu!newsfeed.internetmci.com!in2.uu.net!01-newsfeed.univie.ac.at!03-newsfeed.univie.ac.at!fstgal00.tu-graz.ac.at!balu.kfunigraz.ac.at!usenet From: "E. Haslinger" Newsgroups: bionet.structural-nmr Subject: postdoctoral position Date: Tue, 22 Oct 1996 16:22:09 +0200 Organization: Karl-Franzens-Universität Graz Austria Lines: 12 Message-ID: <326CD891.52D8@kfunigraz.ac.at> Reply-To: Universitätsplatz, 1, A-8010, Graz, Austria NNTP-Posting-Host: bipc18.kfunigraz.ac.at Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.0 (Win95; I) Postdoctoral position availible in structural NMR spectroscopy. Research focuses on investigation of receptor binding of pharmaceutical compounds using transferred NOE. Applicants must have a doctorate in chemistry, biochemistry, physics or biology and a strong background in NMR. Please send CV, names and telephone number of 3 references to: Ernst Haslinger Institut für Pharmazeutische Chemie Karl-Franzens-Universität Graz Universitätsplatz 1 A-8010 Graz Austria Phone: ++43 316 380 5365 Fax: ++43 316 9846 e-mail: ernst.haslinger@kfunigraz.ac.at From owner-structural-nmr@net.bio.net Mon Oct 21 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!news.sprintlink.net!news-peer.sprintlink.net!uunet!in3.uu.net!news.structured.net!news.proaxis.com!news.rain.net!europa62.europa.com From: sethb@europa.com (Seth Birkholz) Newsgroups: bionet.structural-nmr Subject: Wanted: old used electromagnet (such as an NMR magnet) Date: Tue, 22 Oct 1996 01:05:32 GMT Organization: RAINet Lines: 16 Message-ID: <326c1c63.0@atheria.europa.com> NNTP-Posting-Host: atheria.europa.com X-Newsreader: Forte Free Agent 1.0.82 I need an old NMR magnet or any electromagnet with the following minimum specs: 2000 gauss or more 2.5" pole face separation or more 6" pole diameter or more Please respond even if you think you have something close that might be modified. Thank you Seth Birkholz sethb@europa.com 1-800-296-0681 From owner-structural-nmr@net.bio.net Tue Oct 22 23:00:00 1996 Path: biosci!agate!spool.mu.edu!howland.erols.net!www.nntp.primenet.com!nntp.primenet.com!tank.news.pipex.net!pipex!dish.news.pipex.net!pipex!newshost.zeneca.co.uk!usenet From: Paul Stanley Newsgroups: bionet.structural-nmr Subject: position available Date: Wed, 23 Oct 1996 10:32:25 -0700 Organization: zeneca agrochemicals Lines: 37 Message-ID: <326E56A9.5BCC@gbjha.zeneca.com> NNTP-Posting-Host: 156.71.65.108 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; I) Zeneca Agrochemicals have a permanent position available at their UK Research Laboratory for an experienced NMR spectroscopist. Key tasks include structural elucidation and studying the mode of action of biologically significant molecules, project work applying the unique features of NMR and developing and integrated approach to the analysis of bio-molecules. Instrumentation available includes a recently commissioned Varian Inova 500. Ideal candidate will be qualified to PhD with post-doctoral experience in applying NMR methodologies to biological systems. Alternatively chemistry / biochemistry graduates with substantial experience as recognised specialists will be considered. Also required is skill with computer systems and an imaginative approach to problem solving and excellent communication skills. As a specialist in an international organisation with a research centre in California, willingness to travel and a desire to be pro-active in building relationships with scientists from a wide range of backgrounds and locations is essential. Starting salary is up to GBP 30K. This position has the potential to lead to a higher level appointment in scientific leadership. Zeneca is committed to scientific excellence and has a culture with encourages people to be bold and imaginative. We believe that valuing individuals from different backgrounds and experience will lead to improved business performance. Closing date for applications is 8 November 1996. Please e-mail me for further information or apply in writing with a full CV and covering letter to: Penny Hodge, Ref FORM 15/NS Zeneca Agrochemicals PO Box 303 Bracknell RG12 6YX UK From owner-structural-nmr@net.bio.net Thu Oct 24 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!news-peer.gsl.net!news.gsl.net!portc01.blue.aol.com!newsxfer2.itd.umich.edu!news.itd.umich.edu!ramamoor From: ramamoor@choplifter.rs.itd.umich.edu (Ayyalusamy Ramamoorthy) Newsgroups: bionet.structural-nmr Subject: "POSTDOCTORAL POSITION" Date: 25 Oct 1996 15:15:12 GMT Organization: University of Michigan Lines: 56 Message-ID: <54qli0$k9a@lastactionhero.rs.itd.umich.edu> NNTP-Posting-Host: choplifter.rs.itd.umich.edu POSTDOCTORAL POSITION ********************* We are looking for post-doctoral fellows to work on the methodological development of solid-state NMR spectroscopy in the Department of Chemistry and Biophysics Research Division at the University of Michigan, Ann Arbor, Michigan, USA. This research program orchestrates the theoretical design, experimental demonstration, and application of new and cutting edge solid-state NMR spectroscopic methods to study the structure and properties of molecules in single crystalline, liquid crystalline, polycrystalline, and amorphous phases. The design of solid-state NMR methods is composed of a variety of sophisticated techniques including specifically constructed multiple radio-frequency pulses, multi-frequency dimensions, magic-angle spinning, multiple resonance schemes, sensitivity enhancement procedures, selective observation or a hybridization of them. This basic research on spin physics encompasses theoretical and experimental aspects of spin engineering, computer simulations, and instrumentation. We are particularly interested in identifying a bright, hard-working candidate with expertise on spin dynamics, computer programing, simulating solid-state NMR experimental results, instrumentation, applications of solid-state NMR spectroscopy to biological molecules and polymers. The department has 200, 300, 360, & 500 MHz NMR spectrometers, FTIR, CD, spectrophotometers, peptide synthesizer, HPLC, EPR (Q band), Raman, several Silicon Graphics computers, and facilities for molecular biology work (including gene cloning, protein expression, isolation and purification). A three-rf channel 400 MHz solid-state NMR spectrometer will be installed in January 1997. Application including CV, a list of publications, and two Greference letters should be sent to the following address. A. Ramamoorthy e.mail: ramamoor@umich.edu Assistant Professor Department of Chemistry Tel: (313)647-6572 The University of Michigan Fax: (313)747-4865 Ann Arbor, MI 48109. ****************************************************************** Related research papers: 1. A. Ramamoorthy, C. H. Wu and S. J. Opella, Three-Dimensional Solid-State NMR Experiment That Correlates the Chemical Shift and Dipolar Coupling Frequencies of Two Heteronuclei, J. Magn. Reson., B107, 88-90 (1995). 2. A. Ramamoorthy, L.M. Gierasch, and S. J. Opella, Four- Dimensional Solid-State NMR Experiment That Correlates the Chemical-Shift and Dipolar-Coupling Frequencies of Two Heteronuclei with the Exchange of Dilute-Spin Magnetization, J. Magn. Reson., B109, 112-116 (1995). 3. A. Ramamoorthy, F. Marassi, M. Zaslof, and S. J. Opella, Three-Dimensional Solid-State NMR Spectroscopy of a Peptide Oriented in Membrane Bilayers, J. Biol. NMR, 6, 329-334 (1995). _________________________________________________________________ From owner-structural-nmr@net.bio.net Thu Oct 24 23:00:00 1996 Path: biosci!synbio.tpgnet.net!saudekv From: saudekv@synbio.tpgnet.net ("Vladimir Saudek") Newsgroups: bionet.structural-nmr Subject: new address Date: 25 Oct 1996 01:27:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <1395.85662035@mail.synbio.tpgnet.net> NNTP-Posting-Host: net.bio.net Please note my new address: From owner-structural-nmr@net.bio.net Sun Oct 27 22:00:00 1996 Path: biosci!SGI3.MAGNET.FSU.EDU!tian From: tian@SGI3.MAGNET.FSU.EDU (Fang Tian) Newsgroups: bionet.structural-nmr Subject: subscribe Date: 28 Oct 1996 11:29:04 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <9610281915.AA18532@sgi3.magnet.fsu.edu> NNTP-Posting-Host: net.bio.net subscribe From owner-structural-nmr@net.bio.net Mon Oct 28 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!news-peer.sprintlink.net!news-peer.gsl.net!news.gsl.net!portc01.blue.aol.com!newsstand.cit.cornell.edu!news.acsu.buffalo.edu!acsu.buffalo.edu!usenet From: Brian M Burkhart Newsgroups: bionet.structural-nmr Subject: back-calculation program Date: Tue, 29 Oct 1996 10:19:56 -0500 Organization: Hauptman-Woodward Medical Research Institute Lines: 11 Message-ID: <3276209C.41C6@hwi.buffalo.edu> NNTP-Posting-Host: galen.hwi.buffalo.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02S (X11; I; IRIX64 6.2 IP28) I would like to obtain information regarding the availability of NMR back-calculation programs, both commercial (less-desirable) and gratis (most desirable). If you could please email me directly to discuss this matter I would be most appreciative. -- Brian M Burkhart, Ph.D. Hauptman-Woodward Medical Research Institute 73 High Street Buffalo, NY 14203 Phone: (716)856-9600 x313 FAX: (716)852-6086 From owner-structural-nmr@net.bio.net Mon Oct 28 22:00:00 1996 Path: biosci!MSI.COM!ssz From: ssz@MSI.COM (Sandor Szalma) Newsgroups: bionet.structural-nmr Subject: Re: back-calculation program Date: 29 Oct 1996 12:17:02 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <199610292016.MAA26641@iris108.msi.com> References: <3276209C.41C6@hwi.buffalo.edu> NNTP-Posting-Host: net.bio.net >> Brian M Burkhart wrote: >> I would like to obtain information regarding the availability of NMR >> back-calculation programs, Hi Brian, There are couple of commercial options available for back-calculating NOE spectra (if that is what you meant) from MSI: in Felix-Model you can efficiently back-calculate 2D and 3D NOE spectra using the matrix doubling methodology ( P. Yip, J. Biomol. NMR, 3, 361 (1993)) and then visualize and compare them with experimental spectra. in InsightII/NMR-Refine you can back-calculate 2D NOE spectra using either matrix doubling or the interface to IRMA package (R. Boelens et al, J. Magn. Reson. 82, 290 (1989)) where you can use full relaxation matrix approach or two-spin approximation. Cheers, Sandor \~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/ * Sandor Szalma, Ph.D. * * Manager, Analytical Chemistry & email: ssz@msi.com * * Structure Determination tel.: 619-546-5503 * * Molecular Simulations, Inc. http://www.msi.com * * 9685 Scranton Rd, San Diego CA 92121 * /~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~: From owner-structural-nmr@net.bio.net Tue Oct 29 22:00:00 1996 Path: biosci!rutgers!news.sgi.com!howland.erols.net!swrinde!ihnp4.ucsd.edu!scripps.edu!cauchy!case From: case@cauchy.NoSubdomain.NoDomain (David Case) Newsgroups: bionet.structural-nmr Subject: Re: back-calculation program Date: 30 Oct 1996 17:04:09 GMT Organization: The Scripps Research Institute, La Jolla, CA Lines: 25 Sender: case@cauchy (David Case) Distribution: world Message-ID: <5581q9$n3n@riscsm.scripps.edu> References: <3276209C.41C6@hwi.buffalo.edu> NNTP-Posting-Host: cauchy.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit In article <3276209C.41C6@hwi.buffalo.edu>, Brian M Burkhart writes: |> I would like to obtain information regarding the availability of NMR |> back-calculation programs, both commercial (less-desirable) and gratis |> (most desirable). If you could please email me directly to discuss this |> matter I would be most appreciative. The AMBER molecular simulation package has rudimentary but workable routines for backcalculation of 2D NOESY and ROESY spectra (limited to protons unless you want to write some code.) Outputs are to Felix .smx and .mat files. See http://www.amber.ucsf.edu/amber/amber.html or send me mail for more detailed info. Amber requires a license agreement and payment. ....dave case ================================================================== David A. Case | internet: case@scripps.edu Dept. of Molecular Biology, MB1 | bitnet: case%scripps.edu@sdsc The Scripps Research Institute | fax: 619-784-8896 10666 N. Torrey Pines Rd. | phone: 619-784-9768 La Jolla CA 92037 USA | WWW: http://scripps.edu/case ================================================================== From owner-structural-nmr@net.bio.net Tue Oct 29 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: bryan@bor.fkem2.lth.se (Bryan Finn) Newsgroups: bionet.structural-nmr Subject: Re: back-calculation program Date: 30 Oct 1996 12:38:50 -0000 Lines: 33 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <557i8q$2p6@mserv1.dl.ac.uk> Original-To: ssz@MSI.COM Sandor, Sandor Szalma wrote: > in Felix-Model you can efficiently back-calculate 2D and 3D NOE spectra > using the matrix doubling methodology ( P. Yip, J. Biomol. NMR, 3, 361 > (1993)) and then visualize and compare them with experimental spectra. I have recently tried this method without much luck though. I suspect that there is a conflict with naming in my peaks entity and my coordinate file, the latter of which is produced with XPLOR. It says in the Felix-Model manual that Model uses DSPACE (.pdb) convention for peak naming. The problem is: there is no desciption of what the DSPACE convention is in the Felix95 manual. (Yes, I only have Felix and not Insight II). Can you help me on that point? Thanks in advance. Bryan Finn ___________________________________________________________________ | | | Dr. Bryan Finn | | Department of Physical Chemistry 2 Tel: +46-46-222-8254 | | Chemical Center Fax: +46-46-222-4543 | | University of Lund | | POB 124 | | S-221 00 Lund Sweden e-mail: bryan@bor.fkem2.lth.se | | WWW: http://www.fkem2.lth.se/personnel/bryan/finn.html | |_________________________________________________________________| From owner-structural-nmr@net.bio.net Tue Oct 29 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.structural-nmr Subject: Re: back-calculation program Date: 30 Oct 1996 13:57:31 -0000 Lines: 74 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <557msb$7jr@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk Dear Netters, You can also check the program CROWD (ftp://tome.cbs.univ-montp1.fr/pub/CROWD/). This program was developed on the same basis than the NMR data-processing program Gifa, and is free for academic laboratories, after signing a license. I am interested by any suggestions and comments to improve it. Here is a brief description of the program: Sincerely, Theresa E. Malliavin Presentation The Crowd program is a program designed for the NMR relaxation intensity simulation (nOe, rOe,...) and the iterative inter-atomic distance calculation using the experimental NMR intensities. The program was built using the Crowd command parsor and internal langage. Thus, as in Gifa, a complete macro language permits to builds sophisticated processing. The Graphic User Interface is fully designable and programmable by the user. The program currently runs on HP workstations. The graphics can be displayed on X-Windows terminals. This version V1.0 is not stabilised yet, this distribution is still a beta version. This version is distributed under a licence. There is no fees for academic laboratories, however the licence requires that you refer to Crowd in any published work which depend in some manner on the Crowd program.This program can be downloaded by anonymous FTP on Internet, the home site is the following address : ftp://tome.cbs.univ-montp1.fr/pub/CROWD/crowd_v1. Classical processing includes : =============================== o Manipulating the differents NMR relaxation objects (coordinates, distances, relaxation rates, ...) by a set of modular ommands. o Availability of several motion models: isotropic-rigid, Lipari-Szabo, local correlation time models. o Aptitude to read free-format coordinate files. o Aptitude to define hydrogen CH2 and methyl group, by residu name, and group atom names. This allows calculation on various kind of biomolecules: proteins, DNA, RNA, glycoproteins... A Complete set of Macro including: =================================== o simulation of nOe, rOe and off-resonance ROESY intensities from a free-format coordinate file. o implementation of the algorithms proposed in the MARDIGRAS and IRMA programs. The User Interface is characterised by : o Most command are available through a graphic interface o Interactive commands for beginners as well as fast entry mode for advanced users o Complete on-line HELP. o Comprehensive manual. o Versatile command parser which permits to build macro commands with alias, tests, local and global variables, loops, graphic interaction and display capabilities, support for data-bases and associative arrays. o graphical interface completely modifiable and definable by the user. o Possibility to run in interactive mode as well as Batch mode (display less). o The operating system is fully available from Crowd. _________________________________________________________________________ NOTE THAT TELEPHONE NUMBERS IN FRANCE HAVE CHANGED ON THE 18th OCTOBER MY NEW TELEPHONE NUMBERS ARE GIVEN BELOW _________________________________________________________________________ Theresa E. Malliavin terez@tome.cbs.univ-montp1.fr Centre de Biochimie Structurale tel: 33 (0)4 67 04 34 36 Faculte de Pharmacie fax: 33 (0)4 67 52 96 23 15, av. Ch. Flahault F-34060 Montpellier From owner-structural-nmr@net.bio.net Tue Oct 29 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: Marc-Andre Delsuc Newsgroups: bionet.structural-nmr Subject: The GIFA NMR software Date: 30 Oct 1996 18:19:17 -0000 Lines: 90 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <558675$obe@mserv1.dl.ac.uk> Original-To: str-nmr@dl.ac.uk Hi all Netters, GIFA is an NMR processing program that runs on most UNIX machine. It as been around for quite a time now, and the version 4.0 was announced about a year and a half ago. A new version of the Gifa is now available : Version 4.10 - dated 15 october 1996 Check the WEB home-page : http://www.cbs.univ-montp1.fr/GIFA/ (you will find screen snap-shots, macro example, the complete manual (more than 200 pages all together), etc...) ============================================================================== NEW with this version --------------------- The most prominent new features of this version includes : - a new assignment module - extended the use of data-bases - Graphic User Interface have been renewed and extended ============================================================================== SHORT PRESENTATION OF GIFA -------------------------- The Gifa program is a multi-purpose NMR program. It is designed for the processing, the display and the analysis of 1D, 2D & 3D NMR data-sets. The program includes all the classical processing, displaying and plotting capabilities of an NMR program, as well as more advanced processing techniques such as Maximum Entropy processing or Linear prediction. There is no actual limit to the size of the data-set which can be processed. A complete macro language permits to builds sophisticated processing. The Graphic User Interface is fully designable and programmable by the user. An assignment module has recently be added to the program. It is aimed toward the assignment of protein and peptides from a set of 2D homonuclear experiments. The program currently runs on most UNIX platforms. The graphics can be displayed on X-Windows terminals. Plots are generated on postscript or HP-GL devices. There is support for processing files coming from Varian and Bruker (AM, AMX, DMX) spectrometers, as well as more generic formats (ascii format, matlab (tm) files, etc..). ============================================================================== DISTRIBUTION ------------ This version is distributed under a licence. There is no fees for academic laboratories, however the licence requires that you refer to Gifa in any published work which depend in some manner on the Gifa program. The program, as distributed is fully workable, a small annoying message just recall you to ask for a licence. This program can be downloaded by anonymous FTP on Internet, the home site is the following address : ftp://www.cbs.univ-montp1.fr/pub/gifa_v4 There is also mirror sites : In Japan : at Institute for Molecular Science, Okazaki, ftp://ftp.ims.ac.jp/pub/unix/chem/gifa gopher://gopher.ims.ac.jp:70/11/tmp/pub-link/unix/chem/gifa In US. : Ohio Supercomputer Center, Colombus ftp://ccl.osc.edu/pub/chemistry/software/UNIX/gifa/ Only the HP, SGI, Solaris and AIX versions are available now, other versions (Linux) should follow soon (if no problem arise) Best Regards M.A.Delsuc _________________________________________________________________________ Marc-Andre' Delsuc Centre de Biochimie Structurale Marc-Andre.Delsuc@cbs.univ-montp1.fr Faculte de Pharmacie tel : (33) (0)4 67 04 34 36 15 av, Charles Flahault fax : (33) (0)4 67 52 96 23 34060 Montpellier cedex www : http://www.cbs.univ-montp1.fr FRANCE From owner-structural-nmr@net.bio.net Tue Oct 29 22:00:00 1996 Path: biosci!rutgers!csn!nntp-xfer-1.csn.net!magnus.acs.ohio-state.edu!infoserver.bgsu.edu!dad.bgsu.edu!dychen From: dychen@dad.bgsu.edu (Deng-Ywan Chen) Newsgroups: bionet.structural-nmr Subject: deuterated sample Date: 30 Oct 1996 18:46:08 GMT Organization: Bowling Green State Univ. Lines: 4 Distribution: world Message-ID: <5587pg$rpm@infoserver.bgsu.edu> NNTP-Posting-Host: ernie.bgsu.edu hello everyone, can any of you suggest a good source of purchasing ~2g of deuterated (methyl-d3) methacrylate? all info. are appreciated. chen From owner-structural-nmr@net.bio.net Tue Oct 29 22:00:00 1996 Path: biosci!COSY.UTMB.EDU!bruce From: bruce@COSY.UTMB.EDU ("Bruce A. Luxon") Newsgroups: bionet.structural-nmr Subject: NMR back-calculation program Date: 30 Oct 1996 09:36:40 -0800 Organization: Sealy Center for Structural Biology Lines: 54 Sender: daemon@net.bio.net Distribution: world Message-ID: <9610301136.ZM15621@cosy.utmb.edu> Reply-To: bruce@nmr.utmb.edu NNTP-Posting-Host: net.bio.net Back calculations can be performed using the program MORASS which is freely available from David Gorenstein's group in the Sealy Center for Structural Biology at the University of Texas Medical Branch. Please see http://www.nmr.utmb.edu/ for details on MORASS and to download a program package. The program MORASS (Multispin Overhauser Relaxation AnalysiS and Simulation) analyzes 2D NOESY data to evaluate cross-relaxation rates, sigma{ij}, from which interproton distances can be obtained. MORASS also calculates a NOESY spectrum given a model structure including proton coordinate positions. These calculations are carried out by matrix methods involving the relaxation rate matrix specified by the set of simultaneous Bloch equations. Bruce > Subject: back-calculation program > Date: Tue, 29 Oct 1996 10:19:56 -0500 > From: Brian M Burkhart > Subject: back-calculation program > To: str-nmr@net.bio.net > > I would like to obtain information regarding the availability of NMR > back-calculation programs, both commercial (less-desirable) and gratis > (most desirable). If you could please email me directly to discuss this > matter I would be most appreciative. > > -- > Brian M Burkhart, Ph.D. > Hauptman-Woodward Medical Research Institute > 73 High Street Buffalo, NY 14203 > Phone: (716)856-9600 x313 FAX: (716)852-6086 > -- *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* * Bruce A. Luxon, Ph.D * * Assistant Professor * * Sealy Center for Structural Biology U * Dept. of Human Biological Chemistry & Genetics T * University of Texas Medical Branch M * Galveston, TX 77555-1157 B * * * (409)747-6802; Fax (409)747-6850 http://www.hbcg.utmb.edu/ * * bruce@nmr.utmb.edu http://www.nmr.utmb.edu/ * *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* From owner-structural-nmr@net.bio.net Thu Oct 31 22:00:00 1996 Path: biosci!Roche.COM!alfred.ross From: alfred.ross@Roche.COM (Alfred Ross) Newsgroups: bionet.structural-nmr Subject: shigemi tubes Date: 1 Nov 1996 00:25:54 -0800 Organization: Roche Basel AG Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <3279B3D1.167E@roche.com> NNTP-Posting-Host: net.bio.net Dear netters, does anybody know the adress of a branch/agency of the shigemi company located in europe where it might be possible to get a catalogue etc. thanks for any hint -- ************************************* Dr. Alfred Ross NMR-Spectroscopist e-mail: alfred.ross@roche.com ******* Phone: CH-(0)61-6887029 * * Fax: CH-(0)61-6887408 * ROCHE * * * Mail: F. Hoffmann-LaRoche AG ******* (A. Ross - PRPS) Postfach CH-4070 Basel ************************************* From owner-structural-nmr@net.bio.net Thu Oct 31 22:00:00 1996 Path: biosci!IQ.USP.BR!chiramos From: chiramos@IQ.USP.BR ("Carlos H. I. Ramos") Newsgroups: bionet.structural-nmr Subject: (none) Date: 1 Nov 1996 11:13:44 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net subscribe